Methanosarcina mazei strain O1M9704, methanogen with novel tubule isolated from estuarine environment

Diversity and distribution of Archaea in global estuarine ecosystems

Estuarine ecosystem is a unique geographical transitional zone between freshwater and seawater, harboring a wide range of microbial communities including Archaea. Although a large number of Archaea have been detected in such ecosystem, the global patterns in archaeal diversity and distribution are extremely scarce. To bridge this gap, we carried out a comprehensive survey of archaeal communities using ca. 4000 publicly available archaeal 16S rRNA gene sequences (>300 bp) collected from 24 estuaries in different latitude regions. These sequences were divided into 1450 operational taxonomic units (OTUs) at 97% identity, suggesting a high biodiversity that increased gradually from the high- to low-latitude estuaries. Phylogenetic analysis showed that estuarine ecosystem was a large biodiversity pool of Archaea that was mainly composed of 12 phyla. Among them, the predominant groups were Bathyarchaeota, Euryarchaeota and Thaumarchaeota. Interestingly, archaeal distribution demonstrated a geographical differentiation in that Thaumarchaeota was dominated in the low-latitude estuaries, Bathyarchaeota in the mid-latitude estuaries, and Euryarchaeota in the high-latitude estuaries, respectively. Furthermore, the majority of the most abundant 20 OTUs demonstrated an overrepresented or underrepresented distribution pattern in some specific estuaries or latitude regions while a few were evenly distributed throughout the estuaries. This pattern indicates a potential selectivity of geographical distribution. In addition, the analysis of environmental parameters suggested that latitude would be one of the major factors driving the distribution of archaeal communities in estuarine ecosystem. This study profiles a clear framework on the diversity and distribution of Archaea in the global estuarine ecosystem and explores the general environmental factors that influence these patterns. Our findings constitute an important part of the exploration of the global ecology of Archaea.

Isolation and characterization of new Methanosarcina mazei strains KOR-3, -4, -5, and -6 from an anaerobic digester using pig slurry

OBJECTIVE

An experiment was conducted to isolate and identify new methanogens in Korea from an anaerobic digester that uses pig slurry.

METHODS

An anaerobic digestate sample was collected from an anaerobic digester using pig slurry. Pre-reduced media were used for the growth and isolation of methanogens. Growth temperature range, pH range, NaCl concentration range, substrate utilization, and antibiotic tolerance were investigated to determine the physiological characteristics of isolated methanogens. The isolates were also examined microscopically for their morphology and Gram-stained. Polymerase chain reaction of 16S rRNA and mcrA gene-based amplicons was used for identification purpose.

RESULTS

Four strains, designated KOR-3, -4, -5, and -6, were isolated and were non-motile, irregular coccoid, and 0.5 to 1.5 μm in diameter. Moreover, the cell walls of isolated strains were Gram-negative. KOR-3 and KOR-4 strains used acetate for methane production but did not use H₂+CO₂, formate, or methanol as a growth substrate KOR-5 and KOR-6 strains utilized acetate, methanol, and trimethylamine for methanogenesis but did not use H₂+CO₂ or formate as a growth substrate. The optimum temperature and pH for growth of four strains were 39°C and 6.8 to 7.2, respectively. The optimum concentration of NaCl for growth of KOR-3, KOR-5, and KOR-6 were 1.0% (w/v). The optimum NaCl concentration for KOR-4 was 0.5% (w/v). All of the strains tolerated ampicillin, penicillin G, kanamycin, streptomycin, and tetracycline; however, chloramphenicol inhibited cell growth. Phylogenetic analysis of 16S rRNA and mcrA genes demonstrated that strains KOR-3, -4, -5, and -6 are related to Methanosarcina mazei (M. mazei, 99% sequence similarity).

CONCLUSION

On the basis of physiological and phylogenetic characteristics, strains KOR-3, -4, -5, and -6 are proposed to be new strains within the genus Methanosarcina, named M. mazei KOR-3, -4, -5, and -6.

Amino Acid and Peptide Utilization Profiles of the Fluoroacetate-Degrading Bacterium Synergistetes Strain MFA1 Under Varying Conditions

Synergistetes strain MFA1 is an asaccharolytic ruminal bacterium isolated based on its ability to degrade fluoroacetate, a plant toxin. The amino acid and peptide requirements of the bacterium were investigated under different culturing conditions. The growth of strain MFA1 and its fluoroacetate degradation rate were enhanced by peptide-rich protein hydrolysates (tryptone and yeast extract) compared to casamino acid, an amino acid-rich protein hydrolysate. Complete utilization and preference for arginine, asparagine, glutamate, glycine, and histidine as free amino acids from yeast extract were observed, while the utilization of serine, threonine, and lysine in free form and peptide-bound glutamate was stimulated during growth on fluoroacetate. A predominant peptide in yeast extract preferentially utilized by strain MFA1 was partially characterized by high-liquid performance chromatography-mass spectrometry as a hepta-glutamate oligopeptide. Similar utilization profiles of amino acids were observed between the co-culture of strain MFA1 with Methanobrevibacter smithii without fluoroacetate and pure strain MFA1 culture with fluoroacetate. This suggests that growth of strain MFA1 could be enhanced by a reduction of hydrogen partial pressure as a result of hydrogen removal by a methanogen or reduction of fluoroacetate.

Rapid identification of haloarchaea and methanoarchaea using the matrix assisted laser desorption/ionization time-of-flight mass spectrometry

The aim of this study was to classify certain environmental haloarchaea and methanoarchaea using matrix assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), and to expand the archaeal mass spectral database. A total of 69 archaea were collected including type strains and samples isolated locally from different environments. For extraction of the haloarchaeal total cell peptides/proteins, a simple method of acetonitrile extraction was developed. Cluster analysis conducted with the MALDI-TOF MS data overcame the high divergence in intragenomic 16S rRNA sequences in haloarchaea and clearly distinguished Methanohalophilus mahii from M. portucalensis. Putative biomarkers that can distinguish several particular archaeal genera were also assigned. In conclusion, this study expands the mass spectral database of peptide/protein fingerprints from bacteria and fungi to the archaea domain and provides a rapid identification platform for environmental archaeal samples.

Methanospirillum psychrodurum sp. nov., isolated from wetland soil

A psychrotolerant methanogenic strain, X-18T, was isolated from the soil of the Madoi wetland at Qinghai, Tibetan plateau, China. Cells were wavy rods (11–62 µm long) with blunt tapered ends and Gram-stain-negative. Strain X-18T grew strictly anaerobically and produced methane exclusively from H2/CO2. Growth occurred in the temperature range of 4–32 °C and optimally at 25 °C. Growth pH ranged from 6.5 to 8.0 and the optimum was 7.0. The G+C content of the genomic DNA of strain X-18T was 44.4 mol%. Phylogenetic analysis based on 16S rRNA gene sequences and the alpha subunit of methyl-coenzyme M reductase indicated that strain X-18T was affiliated to the genus Methanospirillum and was most closely related to Methanospirillum lacunae Ki8-1T, with 96.3 % 16S rRNA gene sequence similarity. However, strain X-18T could be distinguished from the existing species of the genus Methanospirillum by its lower growth temperature and obligate hydrogenotrophic methanogenesis. On the basis of phenotypic characteristics and phylogenetic analysis, strain X-18T represents a novel species of the genus Methanospirillum , for which the name Methanospirillum psychrodurum sp. nov. is proposed and strain X-18T is assigned as the type strain ( = CGMCC 1.5186T = JCM 19216T).

Methanobrevibacter boviskoreani sp. nov., isolated from the rumen of Korean native cattle

Three strictly anaerobic, methanogenic strains JH1(T), JH4 and JH8 were isolated from rumen of the Korean native cattle (HanWoo; Bos taurus coreanae) in South Korea. The colonies were circular, opaque, and slightly yellowish. Phylogenetic analyses of 16S rRNA gene and mcrA (encoding α subunit of methyl-coenzyme M reductase) sequences confirmed the affiliation of the novel strains with the Methanobacteriales, and Methanobrevibacter wolinii SH(T) was the most closely related species. The 16S rRNA gene and mcrA sequence similarities between strains JH1(T), JH4 and JH8 and M. wolinii SH(T) were 96.2 and 89.0 % respectively, and DNA-DNA hybridization of the isolates and M. wolinii DSM 11976(T) showed a 20 % reassociation. Strain JH1(T) exhibited 92 % DNA-DNA relatedness with strains JH4 and JH8, and their 16S rRNA gene and mcrA sequences were identical. Cells stained Gram-positive and were non-motile rods, 1.5-1.8 µm long and 0.6 µm wide. The strains were able to use H2/CO2 and formate. The optimum temperature and pH ranges for growth were 37-40 °C and pH 6.5-7.0. The DNA G+C content of strain JH1(T) was 28 mol%. Based on data from this study using a polyphasic approach, the three strains represent a novel species of genus Methanobrevibacter, for which the name Methanobrevibacter boviskoreani sp. nov. is proposed. The type strain is JH1(T) ( = KCTC 4102(T) = JCM 18376(T)).

Methanogenic archaea isolated from Taiwan's Chelungpu fault

Terrestrial rocks, petroleum reservoirs, faults, coal seams, and subseafloor gas hydrates contain an abundance of diverse methanoarchaea. However, reports on the isolation, purification, and characterization of methanoarchaea in the subsurface environment are rare. Currently, no studies investigating methanoarchaea within fault environments exist. In this report, we succeeded in obtaining two new methanogen isolates, St545Mb(T) of newly proposed species Methanolobus chelungpuianus and Methanobacterium palustre FG694aF, from the Chelungpu fault, which is the fault that caused a devastating earthquake in central Taiwan in 1999. Strain FG694aF was isolated from a fault gouge sample obtained at 694 m below land surface (mbls) and is an autotrophic, mesophilic, nonmotile, thin, filamentous-rod-shaped organism capable of using H(2)-CO(2) and formate as substrates for methanogenesis. The morphological, biochemical, and physiological characteristics and 16S rRNA gene sequence analysis revealed that this isolate belongs to Methanobacterium palustre. The mesophilic strain St545Mb(T), isolated from a sandstone sample at 545 mbls, is a nonmotile, irregular, coccoid organism that uses methanol and trimethylamine as substrates for methanogenesis. The 16S rRNA gene sequence of strain St545Mb(T) was 99.0% similar to that of Methanolobus psychrophilus strain R15 and was 96 to 97.5% similar to the those of other Methanolobus species. However, the optimal growth temperature and total cell protein profile of strain St545Mb(T) were different from those of M. psychrophilus strain R15, and whole-genome DNA-DNA hybridization revealed less than 20% relatedness between these two strains. On the basis of these observations, we propose that strain St545Mb(T) (DSM 19953(T); BCRC AR10030; JCM 15159) be named Methanolobus chelungpuianus sp. nov. Moreover, the environmental DNA database survey indicates that both Methanolobus chelungpuianus and Methanobacterium palustre are widespread in the subsurface environment.

Methanobacterium movens sp. nov. and Methanobacterium flexile sp. nov., isolated from lake sediment

Two mesophilic methanogenic strains, designated TS-2(T) and GH(T), were isolated from sediments of Tuosu lake and Gahai lake, respectively, in the Qaidam basin, Qinghai province, China. Cells of both isolates were rods (about 0.3-0.5×2-5 µm) with blunt rounded ends and Gram-staining-positive. Strain TS-2(T) was motile with one or two polar flagella and used only H(2)/CO(2) for growth and methanogenesis. Strain GH(T) was non-motile, used both H(2)/CO(2) and formate and displayed a variable cell arrangement depending on the substrate: long chains when growing in formate (50 mM) or under high pressure H(2) and single cells under low pressure H(2). Phylogenetic analysis based on 16S rRNA gene sequences placed the two isolates in the genus Methanobacterium. Strain TS-2(T) was most closely related to Methanobacterium alcaliphilum NBRC 105226(T) (96% 16S rRNA gene sequence similarity). Phylogenetic analysis based on the alpha subunit of methyl-coenzyme M reductase also supported the affiliation of the two isolates with the genus Methanobacterium. DNA-DNA relatedness between the isolates and M. alcaliphilum DSM 3387(T) was 39-53%. Hence we propose two novel species, Methanobacterium movens sp. nov. (type strain TS-2(T)=AS 1.5093(T)=JCM 15415(T)) and Methanobacterium flexile sp. nov. (type strain GH(T)=AS 1.5092(T)=JCM 15416(T)).

Methanoculleus hydrogenitrophicus sp. nov., a methanogenic archaeon isolated from wetland soil

An obligately anaerobic, methanogenic archaeon, strain HCT, was isolated from soil of the Zoige wetland on the Tibetan plateau, China. The strain was isolated through construction of an artificial butyrate-degrading consortium in co-culture with a syntrophic bacterium, ‘Syntrophomonas erecta subsp. sporosyntropha’ JCM 13344. Cells of strain HCT were irregular coccoids, 0.8–2 μm in diameter, that occurred singly and utilized only H2/CO2 for growth and methane production. Growth occurred at 18–45 °C (optimum around 37 °C). The pH for growth was 5.0–8.5 (optimal growth around pH 6.6). The G+C content of the genomic DNA was 60.2 mol%. 16S rRNA gene sequence analysis indicated that strain HCT was affiliated to the genus Methanoculleus, with sequence similarities of 94.8–97.2 % to existing members. However, strain HCT was distinguished from described Methanoculleus species by not using formate for growth or methane formation and not requiring acetate as a growth factor. On the basis of phylogenetic analysis and phenotypic characteristics, the novel species Methanoculleus hydrogenitrophicus sp. nov. is proposed, with strain HCT (=CGMCC 1.5146T =JCM 16311T) as the type strain.

Methanobacterium beijingense sp. nov., a novel methanogen isolated from anaerobic digesters

Two methanogenic strains, 8-2T and 4-1, with rod-shaped (0·4–0·5×3–5 μm), non-motile cells, sometimes observed in chains, were isolated from two anaerobic digesters in Beijing, China. The two strains used H2/CO2 and formate for growth and produced methane. The temperature range for growth was 25–50 °C, with fastest growth at 37 °C. The pH ranges for growth and methane production were 6·5–8·0 for strain 8-2T and 6·8–8·6 for strain 4-1, with the fastest growth at pH 7·2 for strain 8-2T and pH 7·5–7·7 for strain 4-1. The G+C content of genomic DNA for strain 8-2T was 38·9 mol%. The similarity levels of the 16S rRNA sequence of strain 8-2T with other species of the genus Methanobacterium ranged from 93·8 to 96·0 %. Based on the phylogenetic analysis and phenotypic characteristics, the novel species Methanobacterium beijingense sp. nov. is proposed, with the type strain 8-2T (=DSM 15999T=CGMCC 1.5011T).